Detecting footprints of selection at duplicated genes in cultivated and wild flowering plant species using population genetics tools

大量研究表明，基因复制和保留在基因组进化中起着重要作用。一些涉及复制和保留动力学的模型试图建立基因复制和适应之间的理论联系。事实上，许多正选择作用于来自不同植物分类群的重复基因的情况可以用系统发育学方法来鉴定。这些方法为长期和/或反复的积极选择提供了确凿的证据。将这种方法应用于被子植物(开花植物)基因组，我和同事们提供了经验证据，证明正向选择对重复基因的作用比对单拷贝基因的作用要频繁得多。然而，使用群体遗传学工具搜索重复基因的最新选择足迹的研究很少。其主要原因是很难从基因组，特别是转录组数据中区分等位基因和基因拷贝。然而，对等位基因和基因重复进行可靠的分类对于群体遗传分析是至关重要的。在这个项目中，我首先计划开发一条区分等位基因和基因拷贝的管道。这将通过开发以前的程序来实现，这些程序用于进一步区分重复基因和单拷贝基因。下一步，我计划应用合适的群体遗传学方法来分析这些重复的基因。具体地说，我想分析ARCAD数据集，其中包含栽培植物及其野生姐妹物种种群的转录本。这个数据集可以识别与适应有关的基因。这项工作将在Nathalie Chantret博士小组中进行，作为ARCAD项目的一部分，该项目提供数据集。ARCAD项目具有独特的结构，因为它是与来自不同领域(如生物信息学、种群遗传学、比较基因组学)的许多科学家合作进行的。因此，我将能够建立一个广泛的科学网络，这将有助于开展这个项目。此外，我将有机会与ARCAD生物信息学团队合作提高我的编程技能，这将对我未来的研究有用。这个项目无疑将帮助我进一步发展我的知识和技能，以便继续研究植物基因复制和基因家族进化这一有趣的话题。

Numerous studies revealed that gene duplication and retention play an important role in genome evolution. Some models dealing with duplication and retention dynamics tried to establish a theoretical link between gene duplication and adaptation. Indeed, many cases of positive selection acting at duplicated genes from different plant taxa could be identified using phylogenetic approaches. These approaches give solid evidence for long term and/or recurring positive selection. Applying such an approach to angiosperm (flowering plant) genomes, my colleagues and I provided empirical evidence that positive selection is acting far more frequently on duplicated genes compared to single-copy genes. However, studies searching for recent selection footprints at duplicated genes using population genetic tools are scarce. The main reason for this is that it is very difficult to distinguish alleles from gene copies in genome and especially transcriptome data. However, a reliable classification of alleles and gene duplicates is essential for population genetic analysis. In this project, I first plan to develop a pipeline to distinguish alleles and gene copies. This will be done by developing previous programs which were used to differentiate between duplicated and single-copy genes further. In the next step, I plan to apply suitable population genetic methods to analyse these duplicates. Specifically, I want to analyse the ARCAD dataset which contains transcriptomes of cultivated plants and populations of their wild sister species. This dataset allows identifying genes responsible for adaptation. This work will be carried out in the group of Dr Nathalie Chantret as part of the ARCAD project, which provides the dataset. The ARCAD project has a unique structure as it is conducted in collaboration with many scientists from various fields (e.g. bioinformatics, population genetics, comparative genomics). Therefore, I will be able to establish a broad scientific network which will be helpful for conducting this project. Additionally, I will have the opportunity to improve my programing skills in collaboration with the ARCAD bioinformatics team which will be useful for my future research. This project will undoubtedly help me to develop my knowledge and skills further in order to continue investigating the interesting topic of gene duplication and gene family evolution in plants.